On 04/12/2024 15:01, Joel Meyerson wrote:
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Hi,
I would like to use the Coot Python interface to refine a model to a cryoEM
map. I'm able to view all of the functions available in the coot module, and I
see that a model and map can be loaded, and output written, as follows:
#script.py
import coot
coot.read_pdb(filename="model.pdb")
coot.read_ccp4_map(filename="map.mrc", is_diff_map_flag=False)
# Refinement steps here
coot.write_pdb_file(imol=0, file_name="out.pdb")
exit()
# Running the script:
coot --no-graphics --script ./script.py
However, I'm unsure of which functions should be called to do refinements. For
example, it would be helpful to know how to refine individual residues, residue
ranges, full chains, or full molecules. Can you assist?
There are two options
(i) Using Coot as you are doing and (ii) using Python with chapi:
https://www.mrc-lmb.cam.ac.uk/lucrezia/libcootapi-documentation/
For the former
import coot
imol = coot.read_pdb("tutorial-modern-coot-0.pdb")
imol_map = coot.read_mtz("rnasa-1.8-all_refmac1.mtz", "FWT", "PHWT",
"W", 0, 0)
residues = []
for i in range(20, 31):
residues.append(["A", i, ""])
coot.set_imol_refinement_map(imol_map)
coot.set_refinement_immediate_replacement(1)
coot.refine_residues_py(imol, residues)
coot.accept_regularizement()
coot.write_pdb_file("refined.pdb")
For the latter - maybe more useful if you are also hooking up some other
python module beasties:
import chapi
coot = chapi.molecules_container_t(True)
coot.set_max_number_of_threads(8)
imol = coot.read_pdb('tutorial-modern.pdb')
imol_map = coot.read_mtz('rnasa-1.8-all_refmac1.mtz', 'FWT', 'PHWT',
'W', False, False)
coot.set_imol_refinement_map(imol_map)
coot.refine_residue_range(imol, 'A', 20, 30, 1000)
coot.write_coordinates(imol, "refined.pdb")
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